deal with new ruff version and next try for tutorial-test.yml

.github/workflows/tutorial-tests.yml

@@ -1,60 +1,43 @@
 name: Test Tutorial
 # following example: https://securitylab.github.com/research/github-actions-preventing-pwn-requests/
 on:
-  workflow_run:
-    workflows: ["Unit tests"]
-    types:
-      - completed
+  push:
+    branches:
+      - main
+
 
 jobs:
   test-tutorial:
-    if: >
-      github.event.workflow_run.event == 'pull_request' &&
-      github.event.workflow_run.conclusion == 'success'
     runs-on: [self-hosted, linux, x64, gpu]
     container:
       image: continuumio/miniconda3
       options: --runtime=nvidia --gpus all
-    permissions:
-      # Read the action that triggered this one
-      actions: read
-      # Allow to write check runs
-      checks: write
-      # Read and update commit statuses
-      statuses: write
     steps:
       - name: Pull code
         uses: actions/checkout@v4
-        with:
-          repository: github.event.workflow_run.head_repository
-          ref: github.event.workflow_run.head_sha
-      - name: Pull wiki
-        uses: actions/checkout@v4
-        with:
-          # Only check the wiki of the calling repo
-          repository: ${{github.repository}}.wiki 
-          path: wiki
       - name: Install dependencies, code, and list everything
         run: |
           conda install -y -c conda-forge python=3 cupy cuda-version=11.8
           python -m pip install coverage mdextractor #mdextractor is new and might need to be replaced later
           python -m pip install .[dev]
           conda list
+      - name: Goto directory
+        run: |
+          cd docs/tutorials
       - name: Grab files needed for tests
         run: |
-          mkdir wiki/dataset
-          mkdir wiki/templates
-          mkdir wiki/results_80S
-          mkdir wiki/results_60S
-          cd wiki/templates
-          cp ../data/6qzp_60S wiki/templates/
+          mkdir dataset
+          mkdir templates
+          mkdir results_80S
+          mkdir results_60S
+          cd templates
+          cp ../data/6qzp_60S.mrc .
           curl https://files.wwpdb.org/pub/emdb/structures/EMD-2938/map/emd_2938.map.gz -o emd_2938.map.gz
           gunzip emd_2938.map.gz
           mv emd_2938.map emd_2938.mrc
           cd ../dataset
           curl -L -O -J -H "X-Dataverse-key:${{ secrets.DATAVERSE_API_TOKEN }}" https://dataverse.nl/api/access/datafiles/384731,384724,384706,384718
           unzip dataverse_files.zip
-          mv tutorial/* .
           cd ../
       - name: Run Tutorial test
         run: |

.pre-commit-config.yaml

@@ -1,10 +1,10 @@
 repos:
   - repo: https://github.com/astral-sh/ruff-pre-commit
     # Ruff version.
-    rev: v0.4.8
+    rev: v0.6.0
     hooks:
       # Run the linter.
       - id: ruff
         args: [ --fix ]
       # Run the formatter.
-      - id: ruff-format
+      - id: ruff-format

docs/benchmarks/defocus_gradient_analysis.ipynb

@@ -13,8 +13,8 @@
     "import numpy as np\n",
     "from scipy.spatial.distance import cdist\n",
     "from scipy.optimize import curve_fit\n",
-    "from scipy.stats import t\n",
-    "sns.set(style='ticks', context='notebook')"
+    "\n",
+    "sns.set(style=\"ticks\", context=\"notebook\")"
    ]
   },
   {
@@ -32,12 +32,12 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "regular = starfile.read('tm_patch_def_reg/9x9_ts_27_particles.star')\n",
-    "inverted = starfile.read('tm_patch_def_inv/9x9_ts_27_particles.star')\n",
+    "regular = starfile.read(\"tm_patch_def_reg/9x9_ts_27_particles.star\")\n",
+    "inverted = starfile.read(\"tm_patch_def_inv/9x9_ts_27_particles.star\")\n",
     "\n",
     "# divide by the standard deviation of the search to express in nr. of sigma\n",
-    "scores_reg = regular['rlnLCCmax'] / regular['rlnSearchStd']\n",
-    "scores_inv = inverted['rlnLCCmax'] / inverted['rlnSearchStd']"
+    "scores_reg = regular[\"rlnLCCmax\"] / regular[\"rlnSearchStd\"]\n",
+    "scores_inv = inverted[\"rlnLCCmax\"] / inverted[\"rlnSearchStd\"]"
    ]
   },
   {
@@ -47,7 +47,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "coord_cols = ['rlnCoordinateX', 'rlnCoordinateY', 'rlnCoordinateZ']\n",
+    "coord_cols = [\"rlnCoordinateX\", \"rlnCoordinateY\", \"rlnCoordinateZ\"]\n",
     "coords_reg = np.array(regular[coord_cols])\n",
     "coords_inv = np.array(inverted[coord_cols])"
    ]
@@ -89,7 +89,7 @@
     }
    ],
    "source": [
-    "cdist(coords_reg, coords_inv, metric='euclidean').min(axis=0)"
+    "cdist(coords_reg, coords_inv, metric=\"euclidean\").min(axis=0)"
    ]
   },
   {
@@ -120,36 +120,52 @@
    "source": [
     "x_size = 510\n",
     "\n",
+    "\n",
     "def quadratic(x, a_2, a_1, a_0):\n",
-    "    return a_2 * x ** 2 + a_1 * x + a_0\n",
+    "    return a_2 * x**2 + a_1 * x + a_0\n",
     "\n",
-    "def plot_fit_ci(x, s, func, ax1, ax2, l):\n",
+    "\n",
+    "def plot_fit_ci(x, s, func, ax1, ax2, label):\n",
     "    p, cov = curve_fit(func, x, s)\n",
     "    sigma = np.sqrt(np.diagonal(cov))\n",
     "    xs = np.linspace(min(x), max(x))\n",
     "    bound_upper = func(xs, *(p + sigma))\n",
     "    bound_lower = func(xs, *(p - sigma))\n",
-    "    trans = plt.gca().transData\n",
-    "    ax1.scatter(x, s, s=10, alpha=.7)\n",
-    "    ax2.plot(xs, func(xs, *p), label=l)\n",
-    "    ax2.fill_between(xs, bound_lower, bound_upper,\n",
-    "                 color = 'black', alpha = 0.07)\n",
+    "    _ = plt.gca().transData\n",
+    "    ax1.scatter(x, s, s=10, alpha=0.7)\n",
+    "    ax2.plot(xs, func(xs, *p), label=label)\n",
+    "    ax2.fill_between(xs, bound_lower, bound_upper, color=\"black\", alpha=0.07)\n",
+    "\n",
     "\n",
-    "fig, ax = plt.subplots(1, 2, figsize=(10,5))\n",
+    "fig, ax = plt.subplots(1, 2, figsize=(10, 5))\n",
     "ax1, ax2 = ax\n",
-    "plot_fit_ci(coords_reg[:, 0] - x_size / 2 , scores_reg, quadratic, ax1, ax2, 'Default defocus handedness')\n",
-    "plot_fit_ci(coords_inv[:, 0] - x_size / 2 , scores_inv, quadratic, ax1, ax2, 'Inverted defocus handedness')\n",
+    "plot_fit_ci(\n",
+    "    coords_reg[:, 0] - x_size / 2,\n",
+    "    scores_reg,\n",
+    "    quadratic,\n",
+    "    ax1,\n",
+    "    ax2,\n",
+    "    \"Default defocus handedness\",\n",
+    ")\n",
+    "plot_fit_ci(\n",
+    "    coords_inv[:, 0] - x_size / 2,\n",
+    "    scores_inv,\n",
+    "    quadratic,\n",
+    "    ax1,\n",
+    "    ax2,\n",
+    "    \"Inverted defocus handedness\",\n",
+    ")\n",
     "ax1.set_xlim(-x_size / 2 + 10, x_size / 2 - 10)\n",
-    "ax1.set_xlabel('Centered x-coordinate')\n",
-    "ax1.set_ylabel(r'Relative $LCC_{max}$ ($\\sigma$)')\n",
+    "ax1.set_xlabel(\"Centered x-coordinate\")\n",
+    "ax1.set_ylabel(r\"Relative $LCC_{max}$ ($\\sigma$)\")\n",
     "ax1.set_ylim(15, 26)\n",
     "ax2.set_xlim(-x_size / 2 + 10, x_size / 2 - 10)\n",
-    "ax2.set_xlabel('Centered x-coordinate')\n",
-    "ax2.set_ylabel(r'Relative $LCC_{max}$ ($\\sigma$)')\n",
+    "ax2.set_xlabel(\"Centered x-coordinate\")\n",
+    "ax2.set_ylabel(r\"Relative $LCC_{max}$ ($\\sigma$)\")\n",
     "ax2.set_ylim(19, 22)\n",
     "plt.legend()\n",
     "plt.tight_layout()\n",
-    "plt.savefig('x_vs_defocus.svg')\n"
+    "plt.savefig(\"x_vs_defocus.svg\")"
    ]
   },
   {
@@ -177,7 +193,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.11.5"
+   "version": "3.10.12"
   }
  },
  "nbformat": 4,